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Stankovic B, Marinkovic F. A novel procedure for selection of molecular descriptors: QSAR model for mutagenicity of nitroaromatic compounds. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:54603-54617. [PMID: 39207617 DOI: 10.1007/s11356-024-34800-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Accepted: 08/22/2024] [Indexed: 09/04/2024]
Abstract
Nitroaromatic compounds (NACs) stand out as pervasive organic pollutants, prompting an imperative need to investigate their hazardous effects. Computational chemistry methods play a crucial role in this exploration, offering a safer and more time-efficient approach, mandated by various legislations. In this study, our focus lay on the development of transparent, interpretable, reproducible, and publicly available methodologies aimed at deriving quantitative structure-activity relationship models and testing them by modelling the mutagenicity of NACs against the Salmonella typhimurium TA100 strain. Descriptors were selected from Mordred and RDKit molecular descriptors, along with several quantum chemistry descriptors. For that purpose, the genetic algorithm (GA), as the most widely used method in the literature, and three alternative algorithms (Boruta, Featurewiz, and ForwardSelector) combined with the forward stepwise selection technique were used. The construction of models utilized the multiple linear regression method, with subsequent scrutiny of fitting and predictive performance, reliability, and robustness through various statistical validation criteria. The models were ranked by the Multi-Criteria Decision Making procedure. Findings have revealed that the proposed methodology for descriptor selection outperforms GA, with Featurewiz showing a slight advantage over Boruta and ForwardSelector. These constructed models can serve as valuable tools for the quick and reliable prediction of NACs mutagenicity.
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Affiliation(s)
- Branislav Stankovic
- Department for Nuclear and Plasma Physics, Vinča Institute of Nuclear Sciences -National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia.
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2
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Desmecht D, Dubois V. Correlation of the Molecular Cross-Sectional Area of Organic Monofunctional Compounds with Topological Descriptors. J Chem Inf Model 2024; 64:3248-3259. [PMID: 38528706 DOI: 10.1021/acs.jcim.3c01787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
The molecular cross-sectional area (σ) has proved to be an interesting molecular measure not only in the field of adsorption phenomena on solids but also in biochemistry, physiology, or surfactant chemistry. The existing methods to estimate the cross-sectional areas are either not readily applicable or can only be applied to a limited number of compounds. The aim of this work was to describe a method, as general as possible, quick and easy to perform. To that end, the molecular cross-sectional areas were correlated with topological indices. The Emmett-Brunauer formula was used to calculate the reference cross-sectional areas (σEB) of 431 compounds. The correlations of the Wiener (W), hyper-Wiener (WW), Balaban (J), and Randić (χ) indices with σEB were compared for n-alkanes as well as branched and cyclic alkanes. Only the Wiener and hyper-Wiener indices correlated well with σEB, with the data being best fitted by power law regression curves. The lower degeneracy of the hyper-Wiener index did not translate into any significant gain of performance when correlated with σEB. Following the parsimony principle, the less complex Wiener index was thus selected to correlate with the σEB of compounds representing 31 other monofunctional and structural families. The integration of all the compound families into a single curve allowed a quick rough estimation of the cross-sectional areas. The specific reference equations σEB = qWp were determined for the 34 selected families, allowing the fast and reliable calculation of the cross-sectional area of any monofunctional compound.
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Affiliation(s)
- Didier Desmecht
- Laboratory of Catalysis and Porous Materials, Labiris, Sustainable Chemistry, 1 Avenue Gryson, B-1070 Brussels, Belgium
| | - Vincent Dubois
- Laboratory of Catalysis and Porous Materials, Labiris, Sustainable Chemistry, 1 Avenue Gryson, B-1070 Brussels, Belgium
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3
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Nath A, Ojha PK, Roy K. QSAR assessment of aquatic toxicity potential of diverse agrochemicals. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2023:1-20. [PMID: 37941423 DOI: 10.1080/1062936x.2023.2278074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 10/24/2023] [Indexed: 11/10/2023]
Abstract
The fast-increasing number of commercially produced chemicals challenges the experimental ecotoxicity assessment methods, which are costly, time-consuming, and dependent on the sacrifice of animals. In this regard, Quantitative Structure-Property/Activity Relationships (QSPR/QSAR) have led the way in developing ecotoxicity assessment models. In this study, QSAR models have been developed using the pEC50 values of 82 diverse agrochemicals or agro-molecules against a planktonic crustacean Daphnia magna with easily interpretable 2D descriptors. Moreover, a link among octanol-water partition coefficient (KOW), bio-concentration factor (BCF), and critical body residue (CBR) has been addressed, and their imputation for the prediction of the toxicity endpoint (EC50) has been done with an objective of the advanced exploration of several ecotoxicological parameters for toxic chemicals. The developed partial least squares (PLS) models were validated rigorously and proved to be robust, sound, and immensely well-predictive. The final Daphnia toxicity model derived from experimental derived properties along with computed descriptors emerged better in statistical quality and predictivity than those obtained solely from computed descriptors. Additionally, the pEC50 and other important properties (log KOW, log BCF, and log CBR) for a set of external agro-molecules, not employed in model development, were predicted to show the predictive ability of the models.
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Affiliation(s)
| | - P K Ojha
- Drug Theoretics and Cheminformatics Laboratory, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - K Roy
- Drug Theoretics and Cheminformatics Laboratory, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
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4
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Speck-Planche A, Kleandrova VV. The latest guidance on the simultaneous design of virtually active and non-hemolytic peptides. Expert Opin Drug Discov 2022; 17:1067-1069. [PMID: 36148498 DOI: 10.1080/17460441.2022.2128756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Alejandro Speck-Planche
- Grupo de Química Computacional y Teórica (QCT-USFQ), Departamento de Ingeniería Química, Universidad San Francisco de Quito, Diego de Robles y vía Interoceánica, Quito, Ecuador
| | - Valeria V Kleandrova
- Laboratory of Fundamental and Applied Research of Quality and Technology of Food Production, Moscow State University of Food Production, Moscow, Russian Federation
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Speck-Planche A, Kleandrova VV. Multi-Condition QSAR Model for the Virtual Design of Chemicals with Dual Pan-Antiviral and Anti-Cytokine Storm Profiles. ACS OMEGA 2022; 7:32119-32130. [PMID: 36120024 PMCID: PMC9476185 DOI: 10.1021/acsomega.2c03363] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 08/19/2022] [Indexed: 06/15/2023]
Abstract
Respiratory viruses are infectious agents, which can cause pandemics. Although nowadays the danger associated with respiratory viruses continues to be evidenced by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) as the virus responsible for the current COVID-19 pandemic, other viruses such as SARS-CoV-1, the influenza A and B viruses (IAV and IBV, respectively), and the respiratory syncytial virus (RSV) can lead to globally spread viral diseases. Also, from a biological point of view, most of these viruses can cause an organ-damaging hyperinflammatory response known as the cytokine storm (CS). Computational approaches constitute an essential component of modern drug development campaigns, and therefore, they have the potential to accelerate the discovery of chemicals able to simultaneously inhibit multiple molecular and nonmolecular targets. We report here the first multicondition model based on quantitative structure-activity relationships and an artificial neural network (mtc-QSAR-ANN) for the virtual design and prediction of molecules with dual pan-antiviral and anti-CS profiles. Our mtc-QSAR-ANN model exhibited an accuracy higher than 80%. By interpreting the different descriptors present in the mtc-QSAR-ANN model, we could retrieve several molecular fragments whose assembly led to new molecules with drug-like properties and predicted pan-antiviral and anti-CS activities.
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Affiliation(s)
- Alejandro Speck-Planche
- Grupo
de Química Computacional y Teórica (QCT-USFQ), Departamento
de Ingeniería Química, Universidad
San Francisco de Quito, Diego de Robles y vía Interoceánica, Quito 170901, Ecuador
| | - Valeria V. Kleandrova
- Laboratory
of Fundamental and Applied Research of Quality and Technology of Food
Production, Moscow State University of Food
Production, Volokolamskoe
shosse 11, 125080, Moscow, Russian Federation
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6
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Incorporating Machine Learning in Computer-Aided Molecular Design for Fragrance Molecules. Processes (Basel) 2022. [DOI: 10.3390/pr10091767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The demand for new novel flavour and fragrance (F&F) molecules has boosted the need for a systematic approach to designing fragrance molecules. However, the F&F-related industry still relies heavily on experimental approaches or on existing databases without considering the consequences resulting from changes in concentration, which could omit potential fragrances. Computer-aided molecular design (CAMD) has great potential to identify novel molecular structures to be used as fragrances. Using CAMD for this purpose requires models to predict the olfaction properties of molecules. A rough set-based machine learning (RSML) approach is used to develop an interpretable predictive model for odour characteristics in this work. New rule-based models are generated from RSML based on the dilution and a number of different topological indices which identify the structure-odour relationship of fragrance molecules. The most prominent rules are selected and formulated as constraints in a CAMD optimisation model. The combination of several rules was able to increase the coverage of different classes of molecules. To model the performance indicators that vary over a range of properties, a disjunctive programming model is also incorporated into the CAMD framework. A case study demonstrates the utilisation of this methodology to design fragrance additives in dishwashing liquid. The results illustrate the capability of the novel RSML and CAMD framework to identify potential fragrance molecules that can be used in consumer products.
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PTML Modeling for Pancreatic Cancer Research: In Silico Design of Simultaneous Multi-Protein and Multi-Cell Inhibitors. Biomedicines 2022; 10:biomedicines10020491. [PMID: 35203699 PMCID: PMC8962338 DOI: 10.3390/biomedicines10020491] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 02/10/2022] [Accepted: 02/15/2022] [Indexed: 02/07/2023] Open
Abstract
Pancreatic cancer (PANC) is a dangerous type of cancer that is a major cause of mortality worldwide and exhibits a remarkably poor prognosis. To date, discovering anti-PANC agents remains a very complex and expensive process. Computational approaches can accelerate the search for anti-PANC agents. We report for the first time two models that combined perturbation theory with machine learning via a multilayer perceptron network (PTML-MLP) to perform the virtual design and prediction of molecules that can simultaneously inhibit multiple PANC cell lines and PANC-related proteins, such as caspase-1, tumor necrosis factor-alpha (TNF-alpha), and the insulin-like growth factor 1 receptor (IGF1R). Both PTML-MLP models exhibited accuracies higher than 78%. Using the interpretation from one of the PTML-MLP models as a guideline, we extracted different molecular fragments desirable for the inhibition of the PANC cell lines and the aforementioned PANC-related proteins and then assembled some of those fragments to form three new molecules. The two PTML-MLP models predicted the designed molecules as potentially versatile anti-PANC agents through inhibition of the three PANC-related proteins and multiple PANC cell lines. Conclusions: This work opens new horizons for the application of the PTML modeling methodology to anticancer research.
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Speck-Planche A, Kleandrova VV, Scotti MT. In Silico Drug Repurposing for Anti-Inflammatory Therapy: Virtual Search for Dual Inhibitors of Caspase-1 and TNF-Alpha. Biomolecules 2021; 11:biom11121832. [PMID: 34944476 PMCID: PMC8699067 DOI: 10.3390/biom11121832] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 11/15/2021] [Accepted: 12/02/2021] [Indexed: 12/27/2022] Open
Abstract
Inflammation involves a complex biological response of the body tissues to damaging stimuli. When dysregulated, inflammation led by biomolecular mediators such as caspase-1 and tumor necrosis factor-alpha (TNF-alpha) can play a detrimental role in the progression of different medical conditions such as cancer, neurological disorders, autoimmune diseases, and cytokine storms caused by viral infections such as COVID-19. Computational approaches can accelerate the search for dual-target drugs able to simultaneously inhibit the aforementioned proteins, enabling the discovery of wide-spectrum anti-inflammatory agents. This work reports the first multicondition model based on quantitative structure–activity relationships and a multilayer perceptron neural network (mtc-QSAR-MLP) for the virtual screening of agency-regulated chemicals as versatile anti-inflammatory therapeutics. The mtc-QSAR-MLP model displayed accuracy higher than 88%, and was interpreted from a physicochemical and structural point of view. When using the mtc-QSAR-MLP model as a virtual screening tool, we could identify several agency-regulated chemicals as dual inhibitors of caspase-1 and TNF-alpha, and the experimental information later retrieved from the scientific literature converged with our computational results. This study supports the capabilities of our mtc-QSAR-MLP model in anti-inflammatory therapy with direct applications to current health issues such as the COVID-19 pandemic.
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Affiliation(s)
- Alejandro Speck-Planche
- Postgraduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, João Pessoa 58051-900, Brazil;
- Correspondence:
| | - Valeria V. Kleandrova
- Laboratory of Fundamental and Applied Research of Quality and Technology of Food Production, Moscow State University of Food Production, Volokolamskoe shosse 11, 125080 Moscow, Russia;
| | - Marcus T. Scotti
- Postgraduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, João Pessoa 58051-900, Brazil;
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Kleandrova VV, Scotti MT, Speck-Planche A. Indirect-Acting Pan-Antivirals vs. Respiratory Viruses: A Fresh Perspective on Computational Multi-Target Drug Discovery. Curr Top Med Chem 2021; 21:2687-2693. [PMID: 34636311 DOI: 10.2174/1568026621666211012110819] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 09/23/2021] [Accepted: 09/23/2021] [Indexed: 12/22/2022]
Abstract
Respiratory viruses continue to afflict mankind. Among them, pathogens such as coronaviruses [including the current pandemic agent known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)] and the one causing influenza A (IAV) are highly contagious and deadly. These can evade the immune system defenses while causing a hyperinflammatory response that can damage different tissues/organs. Simultaneously targeting immunomodulatory proteins is a plausible antiviral strategy since it could lead to the discovery of indirect-acting pan-antiviral (IAPA) agents for the treatment of diseases caused by respiratory viruses. In this context, computational approaches, which are an essential part of the modern drug discovery campaigns, could accelerate the identification of multi-target immunomodulators. This perspective discusses the usefulness of computational multi-target drug discovery for the virtual screening (drug repurposing) of IAPA agents capable of boosting the immune system through the activation of the toll-like receptor 7 (TLR7) and/or the stimulator of interferon genes (STING) while inhibiting key pro-inflammatory proteins, such as caspase-1 and tumor necrosis factor-alpha (TNF-α).
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Affiliation(s)
- Valeria V Kleandrova
- Laboratory of Fundamental and Applied Research of Quality and Technology of Food Production, Moscow State University of Food Production, Volokolamskoe shosse 11, 125080, Moscow. Russian Federation
| | - Marcus T Scotti
- Postgraduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, 58051-900, João Pessoa. Brazil
| | - Alejandro Speck-Planche
- Postgraduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, 58051-900, João Pessoa. Brazil
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Zakharov AB, Tsarenko DK, Ivanov VV. Topological characteristics of iterated line graphs in the QSAR problem: a multigraph in the description of properties of unsaturated hydrocarbons. Struct Chem 2021. [DOI: 10.1007/s11224-021-01737-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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11
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Qiao K, Fu W, Jiang Y, Chen L, Li S, Ye Q, Gui W. QSAR models for the acute toxicity of 1,2,4-triazole fungicides to zebrafish (Danio rerio) embryos. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 265:114837. [PMID: 32460121 DOI: 10.1016/j.envpol.2020.114837] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 04/27/2020] [Accepted: 05/16/2020] [Indexed: 06/11/2023]
Abstract
In recent decades, the 1,2,4-triazole fungicides are widely used for crop diseases control, and their toxicity to wild lives and pollution to ecosystem have attracted more and more attention. However, how to quickly and efficiently evaluate the toxicity of these compounds to environmental organisms is still a challenge. In silico method, such like Quantitative Structure-Activity Relationship (QSAR), provides a good alternative to evaluate the environmental toxicity of a large number of chemicals. At the present study, the acute toxicity of 23 1,2,4-triazole fungicides to zebrafish (Danio rerio) embryos was firstly tested, and the LC50 (median lethal concentration) values were used as the bio-activity endpoint to conduct QSAR modelling for these triazoles. After the comparative study of several QSAR models, the 2D-QSAR model was finally constructed using the stepwise multiple linear regression algorithm combining with two physicochemical parameters (logD and μ), an electronic parameter (QN1) and a topological parameter (XvPC4). The optimal model could be mathematically described as following: pLC50 = -7.24-0.30XvPC4 + 0.76logD - 26.15QN1 - 0.08μ. The internal validation by leave-one-out (LOO) cross-validation showed that the R2adj (adjusted noncross-validation squared correlation coefficient), Q2 (cross-validation correlation coefficient) and RMSD (root-mean-square error) was 0.88, 0.84 and 0.17, respectively. The external validation indicated the model had a robust predictability with the q2 (predictive squared correlation coefficient) of 0.90 when eliminated tricyclazole. The present study provided a potential tool for predicting the acute toxicity of new 1,2,4-triazole fungicides which contained an independent triazole ring group in their molecules to zebrafish embryos, and also provided a reference for the development of more environmentally-friendly 1,2,4-triazole pesticides in the future.
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Affiliation(s)
- Kun Qiao
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Pesticide and Environmental Toxicology, Zhejiang University, Hangzhou, 310058, PR China; Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, 310058, PR China
| | - Wenjie Fu
- Institute of Insect Science, Zhejiang University, Hangzhou, 310058, PR China
| | - Yao Jiang
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Pesticide and Environmental Toxicology, Zhejiang University, Hangzhou, 310058, PR China
| | - Lili Chen
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Pesticide and Environmental Toxicology, Zhejiang University, Hangzhou, 310058, PR China
| | - Shuying Li
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Pesticide and Environmental Toxicology, Zhejiang University, Hangzhou, 310058, PR China
| | - Qingfu Ye
- Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, 310058, PR China
| | - Wenjun Gui
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Pesticide and Environmental Toxicology, Zhejiang University, Hangzhou, 310058, PR China.
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Bumbăcilă B, Putz MV. Neurotoxicity of Pesticides: The Roadmap for the Cubic Mode of Action. Curr Med Chem 2020; 27:54-77. [DOI: 10.2174/0929867326666190704142354] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Revised: 05/08/2019] [Accepted: 06/20/2019] [Indexed: 01/15/2023]
Abstract
Pesticides are used today on a planetary-wide scale. The rising need for substances with this
biological activity due to an increasing consumption of agricultural and animal products and to the
development of urban areas makes the chemical industry to constantly investigate new molecules or to
improve the physicochemical characteristics, increase the biological activities and improve the toxicity
profiles of the already known ones. Molecular databases are increasingly accessible for in vitro and in
vivo bioavailability studies. In this context, structure-activity studies, by their in silico - in cerebro
methods, are used to precede in vitro and in vivo studies in plants and experimental animals because
they can indicate trends by statistical methods or biological activity models expressed as mathematical
equations or graphical correlations, so a direction of study can be developed or another can be abandoned,
saving financial resources, time and laboratory animals. Following this line of research the present paper
reviews the Structure-Activity Relationship (SAR) studies and proposes a correlation between a topological
connectivity index and the biological activity or toxicity made as a result of a study performed on 11 molecules
of organophosphate compounds, randomly chosen, with a basic structure including a Phosphorus atom
double bounded to an Oxygen atom or to a Sulfur one and having three other simple covalent bonds with two
alkoxy (-methoxy or -ethoxy) groups and to another functional group different from the alkoxy groups. The
molecules were packed on a cubic structure consisting of three adjacent cubes, respecting a principle of topological
efficiency, that of occupying a minimal space in that cubic structure, a method that was called the Clef
Method. The central topological index selected for correlation was the Wiener index, since it was possible
this way to discuss different adjacencies between the nodes in the graphs corresponding to the organophosphate
compounds molecules packed on the cubic structure; accordingly, "three dimensional" variants of these
connectivity indices could be considered and further used for studying the qualitative-quantitative relationships
for the specific molecule-enzyme interaction complexes, including correlation between the Wiener
weights (nodal specific contributions to the total Wiener index of the molecular graph) and the biochemical
reactivity of some of the atoms. Finally, when passing from SAR to Q(uantitative)-SAR studies, especially by
the present advanced method of the cubic molecule (Clef Method) and its good assessment of the
(neuro)toxicity of the studied molecules and of their inhibitory effect on the target enzyme - acetylcholinesterase,
it can be seen that a predictability of the toxicity and activity of different analogue compounds can
be ensured, facilitating the in vivo experiments or improving the usage of pesticides.
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Affiliation(s)
- Bogdan Bumbăcilă
- Laboratory of Computational and Structural Physical-Chemistry for Nanosciences and QSAR, Biology- Chemistry Department, Faculty of Chemistry, Biology, Geography at West University of Timisoara, Pestalozzi Street No.16, Timisoara RO-300115, Romania
| | - Mihai V. Putz
- Laboratory of Computational and Structural Physical-Chemistry for Nanosciences and QSAR, Biology- Chemistry Department, Faculty of Chemistry, Biology, Geography at West University of Timisoara, Pestalozzi Street No.16, Timisoara RO-300115, Romania
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Topological Indices of Hyaluronic Acid-Paclitaxel Conjugates’ Molecular Structure in Cancer Treatment. OPEN CHEM 2019. [DOI: 10.1515/chem-2019-0009] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
AbstractA large number of medical experiments have confirmed that the features of drugs have a close correlation with their molecular structure. Drug properties can be obtained by studying the molecular structure of corresponding drugs. The calculation of the topological index of a drug structure enables scientists to have a better understanding of the physical chemistry and biological characteristics of drugs. In this paper, we focus on Hyaluronic Acid-Paclitaxel conjugates which are widely used in the manufacture of anticancer drugs. Several topological indices are determined by virtue of the edge-partition method, and our results remedy the lack of medicine experiments, thus providing a theoretical basis for pharmaceutical engineering.
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14
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Fayet G, Rotureau P. New QSPR Models to Predict the Flammability of Binary Liquid Mixtures. Mol Inform 2019; 38:e1800122. [DOI: 10.1002/minf.201800122] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 12/12/2018] [Indexed: 12/14/2022]
Affiliation(s)
- Guillaume Fayet
- INERISAccidental Risk Division Parc Technologique Alata 60550 Verneuil-en-Halatte France
| | - Patricia Rotureau
- INERISAccidental Risk Division Parc Technologique Alata 60550 Verneuil-en-Halatte France
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15
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Nekrasova NA, Kurbatova SV. Relationship between the structure and physicochemical characteristics of 1,2,3,4-tetrahydroquinoline derivatives. J STRUCT CHEM+ 2017. [DOI: 10.1134/s0022476617040187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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16
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Martínez-Santiago O, Marrero-Ponce Y, Vivas-Reyes R, Rivera-Borroto OM, Hurtado E, Treto-Suarez MA, Ramos Y, Vergara-Murillo F, Orozco-Ugarriza ME, Martínez-López Y. Exploring the QSAR's predictive truthfulness of the novel N-tuple discrete derivative indices on benchmark datasets. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2017; 28:367-389. [PMID: 28590848 DOI: 10.1080/1062936x.2017.1326403] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 04/27/2017] [Indexed: 06/07/2023]
Abstract
Graph derivative indices (GDIs) have recently been defined over N-atoms (N = 2, 3 and 4) simultaneously, which are based on the concept of derivatives in discrete mathematics (finite difference), metaphorical to the derivative concept in classical mathematical analysis. These molecular descriptors (MDs) codify topo-chemical and topo-structural information based on the concept of the derivative of a molecular graph with respect to a given event (S) over duplex, triplex and quadruplex relations of atoms (vertices). These GDIs have been successfully applied in the description of physicochemical properties like reactivity, solubility and chemical shift, among others, and in several comparative quantitative structure activity/property relationship (QSAR/QSPR) studies. Although satisfactory results have been obtained in previous modelling studies with the aforementioned indices, it is necessary to develop new, more rigorous analysis to assess the true predictive performance of the novel structure codification. So, in the present paper, an assessment and statistical validation of the performance of these novel approaches in QSAR studies are executed, as well as a comparison with those of other QSAR procedures reported in the literature. To achieve the main aim of this research, QSARs were developed on eight chemical datasets widely used as benchmarks in the evaluation/validation of several QSAR methods and/or many different MDs (fundamentally 3D MDs). Three to seven variable QSAR models were built for each chemical dataset, according to the original dissection into training/test sets. The models were developed by using multiple linear regression (MLR) coupled with a genetic algorithm as the feature wrapper selection technique in the MobyDigs software. Each family of GDIs (for duplex, triplex and quadruplex) behaves similarly in all modelling, although there were some exceptions. However, when all families were used in combination, the results achieved were quantitatively higher than those reported by other authors in similar experiments. Comparisons with respect to external correlation coefficients (q2ext) revealed that the models based on GDIs possess superior predictive ability in seven of the eight datasets analysed, outperforming methodologies based on similar or more complex techniques and confirming the good predictive power of the obtained models. For the q2ext values, the non-parametric comparison revealed significantly different results to those reported so far, which demonstrated that the models based on DIVATI's indices presented the best global performance and yielded significantly better predictions than the 12 0-3D QSAR procedures used in the comparison. Therefore, GDIs are suitable for structure codification of the molecules and constitute a good alternative to build QSARs for the prediction of physicochemical, biological and environmental endpoints.
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Affiliation(s)
- O Martínez-Santiago
- a Department of Chemical Sciences , Central University 'Martha Abreu' of Las Villas , Santa Clara , Cuba
- b Unit of Computer-Aided Molecular 'Biosilico' Discovery and Bioinformatics Research International Network (CAMD-BIR IN) , Quito , Ecuador
- c Group of Quantum and Theoretical Chemistry , University of Cartagena , Cartagena de Indias , Colombia
- d Facultad de Ingeniería , Grupo CipTec, Fundación Universitaria Tecnológico Comfenalco , Cartagena de Indias , Colombia
| | - Y Marrero-Ponce
- b Unit of Computer-Aided Molecular 'Biosilico' Discovery and Bioinformatics Research International Network (CAMD-BIR IN) , Quito , Ecuador
- e Escuela de Medicina, Edificio de Especialidades Médicas , Universidad San Francisco de Quito (USFQ), Grupo de Medicina Molecular y Traslacional (MeM&T), Colegio de Ciencias de la Salud (COCSA) , Av. Interoceánica Km 12 ½, Cumbayá , Ecuador
- f Instituto de Simulación Computacional (ISC-USFQ), Diego de Robles y vía Interoceánica , Quito , Ecuador
- g Grupo de Investigación Ambiental (GIA) , Fundación Universitaria Tecnológico de Comfenalco , Cartagena de Indias , Colombia
| | - R Vivas-Reyes
- c Group of Quantum and Theoretical Chemistry , University of Cartagena , Cartagena de Indias , Colombia
- d Facultad de Ingeniería , Grupo CipTec, Fundación Universitaria Tecnológico Comfenalco , Cartagena de Indias , Colombia
| | - O M Rivera-Borroto
- b Unit of Computer-Aided Molecular 'Biosilico' Discovery and Bioinformatics Research International Network (CAMD-BIR IN) , Quito , Ecuador
- h Departamento de Química Física Aplicada , Universidad Autónoma de Madrid (UAM) , Madrid , España
| | - E Hurtado
- b Unit of Computer-Aided Molecular 'Biosilico' Discovery and Bioinformatics Research International Network (CAMD-BIR IN) , Quito , Ecuador
| | - M A Treto-Suarez
- i Center of Applied Nanosciences (CENAP), Andres Bello University , Chile
| | - Y Ramos
- j Department of Economic Sciences , University of Camagüey , Camagüey , Cuba
| | - F Vergara-Murillo
- c Group of Quantum and Theoretical Chemistry , University of Cartagena , Cartagena de Indias , Colombia
- d Facultad de Ingeniería , Grupo CipTec, Fundación Universitaria Tecnológico Comfenalco , Cartagena de Indias , Colombia
| | - M E Orozco-Ugarriza
- k Seccional Cartagena y Grupo de Investigación Traslacional en Biomedicina & Biotecnología - GITB&B , Universidad del Sinú - Elías Bechara Zainúm , Cartagena de Indias , Colombia
| | - Y Martínez-López
- b Unit of Computer-Aided Molecular 'Biosilico' Discovery and Bioinformatics Research International Network (CAMD-BIR IN) , Quito , Ecuador
- l Grupo de Investigación de Inteligencia Artificial (AIRES) , Universidad de Camagüey , Camagüey , Cuba
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17
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Dzhabieva SA, Kurbatova SV, Kolosova EA. Effect of the topology of benzotriazole derivatives on their chromatographic retention under RP-HPLC conditions. J STRUCT CHEM+ 2017. [DOI: 10.1134/s0022476617030052] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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18
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Gagorik AG, Savoie B, Jackson N, Agrawal A, Choudhary A, Ratner MA, Schatz GC, Kohlstedt KL. Improved Scaling of Molecular Network Calculations: The Emergence of Molecular Domains. J Phys Chem Lett 2017; 8:415-421. [PMID: 28036172 DOI: 10.1021/acs.jpclett.6b02921] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The design of materials needed for the storage, delivery, and conversion of (re)useable energy is still hindered by the lack of new, hierarchical molecular screening methodologies that encode information on more than one length scale. Using a molecular network theory as a foundation, we show that to describe charge transport in disordered materials the network methodology must be scaled-up. We detail the scale-up through the use of adjacency lists and depth first search algorithms for during operations on the adjacency matrix. We consider two types of electronic acceptors, perylenediimide (PDI) and the fullerene derivative phenyl-C61-butyric acid methyl ester (PCBM), and we demonstrate that the method is scalable to length scales relevant to grain boundary and trap formations. Such boundaries lead to a decrease in the percolation ratio of PDI with system size, while the ratio for PCBM remains constant, further quantifying the stable, diverse transport pathways of PCBM and its success as a charge-accepting material.
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Affiliation(s)
- Adam G Gagorik
- Department of Chemistry, Northwestern University , Evanston, Illinois 60208, United States
| | - Brett Savoie
- Department of Chemistry, Northwestern University , Evanston, Illinois 60208, United States
| | - Nick Jackson
- Department of Chemistry, Northwestern University , Evanston, Illinois 60208, United States
| | - Ankit Agrawal
- Department of Electrical Engineering and Computer Science, Northwestern University , Evanston Illinois 60208, United States
| | - Alok Choudhary
- Department of Electrical Engineering and Computer Science, Northwestern University , Evanston Illinois 60208, United States
| | - Mark A Ratner
- Department of Chemistry, Northwestern University , Evanston, Illinois 60208, United States
| | - George C Schatz
- Department of Chemistry, Northwestern University , Evanston, Illinois 60208, United States
| | - Kevin L Kohlstedt
- Department of Chemistry, Northwestern University , Evanston, Illinois 60208, United States
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19
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Martínez-Santiago O, Marrero-Ponce Y, Barigye SJ, Le Thi Thu H, Torres FJ, Zambrano CH, Muñiz Olite JL, Cruz-Monteagudo M, Vivas-Reyes R, Vázquez Infante L, Artiles Martínez LM. Physico-Chemical and Structural Interpretation of Discrete Derivative Indices on N-Tuples Atoms. Int J Mol Sci 2016; 17:ijms17060812. [PMID: 27240357 PMCID: PMC4926346 DOI: 10.3390/ijms17060812] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Revised: 04/27/2016] [Accepted: 05/04/2016] [Indexed: 11/28/2022] Open
Abstract
This report examines the interpretation of the Graph Derivative Indices (GDIs) from three different perspectives (i.e., in structural, steric and electronic terms). It is found that the individual vertex frequencies may be expressed in terms of the geometrical and electronic reactivity of the atoms and bonds, respectively. On the other hand, it is demonstrated that the GDIs are sensitive to progressive structural modifications in terms of: size, ramifications, electronic richness, conjugation effects and molecular symmetry. Moreover, it is observed that the GDIs quantify the interaction capacity among molecules and codify information on the activation entropy. A structure property relationship study reveals that there exists a direct correspondence between the individual frequencies of atoms and Hückel’s Free Valence, as well as between the atomic GDIs and the chemical shift in NMR, which collectively validates the theory that these indices codify steric and electronic information of the atoms in a molecule. Taking in consideration the regularity and coherence found in experiments performed with the GDIs, it is possible to say that GDIs possess plausible interpretation in structural and physicochemical terms.
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Affiliation(s)
- Oscar Martínez-Santiago
- Computer-Aided Molecular "Biosilico" Discovery and Bioinformatic Research International Network (CAMD-BIR IN), Cumbayá-Tumbaco, Quito 170184, Ecuador.
- Department of Chemical Science, Faculty of Chemistry-Pharmacy, Universidad Central "Martha Abreu" de Las Villas, Santa Clara 54830, Villa Clara, Cuba.
| | - Yovani Marrero-Ponce
- Computer-Aided Molecular "Biosilico" Discovery and Bioinformatic Research International Network (CAMD-BIR IN), Cumbayá-Tumbaco, Quito 170184, Ecuador.
- Universidad San Francisco de Quito (USFQ), Grupo de Medicina Molecular y Traslacional (MeM&T), Colegio de Ciencias de la Salud (COCSA), Escuela de Medicina, Edificio de Especialidades Médicas, Hospital de los Valles, Av. Interoceánica Km 12 ½-Cumbayá, Quito 170157, Ecuador.
- Universidad San Francisco de Quito (USFQ), Instituto de Simulación Computacional (ISC-USFQ), Diego de Robles y vía Interoceánica, Quito 170157, Ecuador.
- Grupo de Investigación Microbiología y Ambiente (GIMA), Programa de Bacteriología, Facultad Ciencias de la Salud, Universidad de San Buenaventura, Calle Real de Ternera, Cartagena de Indias, Bolívar 130010, Colombia.
| | - Stephen J Barigye
- Computer-Aided Molecular "Biosilico" Discovery and Bioinformatic Research International Network (CAMD-BIR IN), Cumbayá-Tumbaco, Quito 170184, Ecuador.
- Departamento de Química, Universidade Federal de Lavras (UFLA), Caixa Postal 3037, Lavras 37200-000, MG, Brazil.
| | - Huong Le Thi Thu
- School of Medicine and Pharmacy, Vietnam National University, Hanoi (VNU) 144 Xuan Thuy, Cau Giay, Hanoi 100000, Vietnam.
| | - F Javier Torres
- Universidad San Francisco de Quito (USFQ), Instituto de Simulación Computacional (ISC-USFQ), Diego de Robles y vía Interoceánica, Quito 170157, Ecuador.
- Universidad San Francisco de Quito (USFQ), Grupo de Química Computacional y Teórica (QCT-USFQ), Departamento de Ingeniería Química, Diego de Robles y Vía Interoceánica, Quito 170157, Ecuador.
| | - Cesar H Zambrano
- Universidad San Francisco de Quito (USFQ), Instituto de Simulación Computacional (ISC-USFQ), Diego de Robles y vía Interoceánica, Quito 170157, Ecuador.
- Universidad San Francisco de Quito (USFQ), Grupo de Química Computacional y Teórica (QCT-USFQ), Departamento de Ingeniería Química, Diego de Robles y Vía Interoceánica, Quito 170157, Ecuador.
| | - Jorge L Muñiz Olite
- Grupo de Investigación en Estudios Químicos y Biológicos, Facultad de Ciencias Básicas, Universidad Tecnológica de Bolívar (UTB), Parque Industrial y Tecnológico Carlos Vélez Pombo Km 1 vía Turbaco, Cartagena de Indias, Bolívar 130010, Colombia.
| | - Maykel Cruz-Monteagudo
- Instituto de Investigaciones Biomédicas (IIB), Universidad de Las Américas (UDLA), Quito 170513, Ecuador.
| | - Ricardo Vivas-Reyes
- Grupo de Química Cuántica y Teórica, Facultad de Ciencias, Universidad de Cartagena, Cartagena de Indias, Bolívar 130001, Colombia.
- Grupo CipTec, Fundación Universitaria Tecnológico de Comfenalco, Facultad de Ingenierías, Programa de Ingeniería de Procesos, Cartagena de Indias, Bolívar 130001, Colombia.
| | - Liliana Vázquez Infante
- Computer-Aided Molecular "Biosilico" Discovery and Bioinformatic Research International Network (CAMD-BIR IN), Cumbayá-Tumbaco, Quito 170184, Ecuador.
- Department of Chemical Science, Faculty of Chemistry-Pharmacy, Universidad Central "Martha Abreu" de Las Villas, Santa Clara 54830, Villa Clara, Cuba.
| | - Luis M Artiles Martínez
- Computer-Aided Molecular "Biosilico" Discovery and Bioinformatic Research International Network (CAMD-BIR IN), Cumbayá-Tumbaco, Quito 170184, Ecuador.
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20
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Speck-Planche A, Kleandrova VV, Ruso JM, Cordeiro MNDS. First Multitarget Chemo-Bioinformatic Model To Enable the Discovery of Antibacterial Peptides against Multiple Gram-Positive Pathogens. J Chem Inf Model 2016; 56:588-98. [PMID: 26960000 DOI: 10.1021/acs.jcim.5b00630] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Antimicrobial peptides (AMPs) have emerged as promising therapeutic alternatives to fight against the diverse infections caused by different pathogenic microorganisms. In this context, theoretical approaches in bioinformatics have paved the way toward the creation of several in silico models capable of predicting antimicrobial activities of peptides. All current models have several significant handicaps, which prevent the efficient search for highly active AMPs. Here, we introduce the first multitarget (mt) chemo-bioinformatic model devoted to performing alignment-free prediction of antibacterial activity of peptides against multiple Gram-positive bacterial strains. The model was constructed from a data set containing 2488 cases of AMPs sequences assayed against at least 1 out of 50 Gram-positive bacterial strains. This mt-chemo-bioinformatic model displayed percentages of correct classification higher than 90.00% in both training and prediction (test) sets. For the first time, two computational approaches derived from basic concepts in genetics and molecular biology were applied, allowing the calculations of the relative contributions of any amino acid (in a defined position) to the antibacterial activity of an AMP and depending on the bacterial strain used in the biological assay. The present mt-chemo-bioinformatic model constitutes a powerful tool to enable the discovery of potent and versatile AMPs.
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Affiliation(s)
- Alejandro Speck-Planche
- Department of Applied Physics, University of Santiago de Compostela (USC) , 15782 Santiago de Compostela, Spain.,REQUIMTE/Department of Chemistry and Biochemistry, University of Porto , 4169-007 Porto, Portugal
| | - Valeria V Kleandrova
- Faculty of Technology and Production Management, Moscow State University of Food Production , Volokolamskoe shosse 11, 125080 Moscow, Russia
| | - Juan M Ruso
- Department of Applied Physics, University of Santiago de Compostela (USC) , 15782 Santiago de Compostela, Spain
| | - M N D S Cordeiro
- REQUIMTE/Department of Chemistry and Biochemistry, University of Porto , 4169-007 Porto, Portugal
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21
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Szczepański P. A new method for estimation of the overall mass transfer coefficient in pertraction. Chem Eng Res Des 2016. [DOI: 10.1016/j.cherd.2015.12.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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22
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Pingaew R, Prachayasittikul V, Worachartcheewan A, Nantasenamat C, Prachayasittikul S, Ruchirawat S, Prachayasittikul V. Novel 1,4-naphthoquinone-based sulfonamides: Synthesis, QSAR, anticancer and antimalarial studies. Eur J Med Chem 2015; 103:446-59. [DOI: 10.1016/j.ejmech.2015.09.001] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Revised: 08/11/2015] [Accepted: 09/02/2015] [Indexed: 11/28/2022]
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23
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Miličević A, Raos N. Graph-Theoretical Modelling of Stability Constants of Copper(II) Complexes with Tripeptides Containing Glycine, Glutamic acid, and Histidine. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2015. [DOI: 10.1246/bcsj.20140358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
| | - Nenad Raos
- Institute for Medical Research and Occupational Health
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24
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Barigye SJ, Marrero-Ponce Y, Zupan J, Pérez-Giménez F, Freitas MP. Structural and Physicochemical Interpretation of GT-STAF Information Theory-Based Indices. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2015. [DOI: 10.1246/bcsj.20140037] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Stephen J. Barigye
- Departamento de Química, Universidade Federal de Lavras, UFLA
- Unit of Computer-Aided Molecular “Biosilico” Discovery and Bioinformatic Research (CAMD-BIR Unit), Faculty of Chemistry-Pharmacy, Universidad Central “Martha Abreu” de Las Villas
| | - Yovani Marrero-Ponce
- Unit of Computer-Aided Molecular “Biosilico” Discovery and Bioinformatic Research (CAMD-BIR Unit), Faculty of Chemistry-Pharmacy, Universidad Central “Martha Abreu” de Las Villas
- Institut Universitari de Ciència Molecular, Universitat de València, Edifici d’Instituts de Paterna
- Unidad de Investigación de Diseño de Fármacos y Conectividad Molecular, Departamento de Química Física, Facultad de Farmacia, Universitat de València
- Facultad de Química Farmacéutica, Universidad de Cartagena
| | - Jure Zupan
- Laboratory of Chemometrics, National Institute of Chemistry
| | - Facundo Pérez-Giménez
- Unidad de Investigación de Diseño de Fármacos y Conectividad Molecular, Departamento de Química Física, Facultad de Farmacia, Universitat de València
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25
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Speck-Planche A, Cordeiro MNDS. A general ANN-based multitasking model for the discovery of potent and safer antibacterial agents. Methods Mol Biol 2015; 1260:45-64. [PMID: 25502375 DOI: 10.1007/978-1-4939-2239-0_4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Bacteria have been one of the world's most dangerous and deadliest pathogens for mankind, nowadays giving rise to significant public health concerns. Given the prevalence of these microbial pathogens and their increasing resistance to existing antibiotics, there is a pressing need for new antibacterial drugs. However, development of a successful drug is a complex, costly, and time-consuming process. Quantitative Structure-Activity Relationships (QSAR)-based approaches are valuable tools for shortening the time of lead compound identification but also for focusing and limiting time-costly synthetic activities and in vitro/vivo evaluations. QSAR-based approaches, supported by powerful statistical techniques such as artificial neural networks (ANNs), have evolved to the point of integrating dissimilar types of chemical and biological data. This chapter reports an overview of the current research and potential applications of QSAR modeling tools toward the rational design of more efficient antibacterial agents. Particular emphasis is given to the setup of multitasking models along with ANNs aimed at jointly predicting different antibacterial activities and safety profiles of drugs/chemicals under diverse experimental conditions.
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Affiliation(s)
- A Speck-Planche
- Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, 4169-007, Porto, Portugal
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26
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Stability prediction of Cu2+, Ni2+ and Zn2+ N-salicylidene-aminoacidato complexes by models based on connectivity index 3 χ v. OPEN CHEM 2014. [DOI: 10.2478/s11532-013-0345-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
AbstractThis paper presents models for the estimation of stability constants (K 1 and β 2) of nickel(II), copper(II) and zinc(II) mono- and bis-complexes with 5 Schiff bases (salicylideneglycine, salicylidenealanine, salicylideneserine, salicylidenephenylalanine, and salicylidenetyrosine). The models were based on the molecular-graph theory and valence molecular connectivity index of the 3rd order, 3χv , derived from it. Univariate linear models were developed for each metal separately, while in the common models for two and three metals, the indicator variable, In, was introduced. The standard error of models for the log K 1 constant was less than 0.12, while for log β 2 models, the S.E. did not exceed 0.14.
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27
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Chemoinformatics for rational discovery of safe antibacterial drugs: simultaneous predictions of biological activity against streptococci and toxicological profiles in laboratory animals. Bioorg Med Chem 2013; 21:2727-32. [PMID: 23582445 DOI: 10.1016/j.bmc.2013.03.015] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Revised: 03/03/2013] [Accepted: 03/04/2013] [Indexed: 11/21/2022]
Abstract
Streptococci are a group of Gram-positive bacteria which are responsible for causing many diverse diseases in humans and other animals worldwide. The high prevalence of resistance of these bacteria to current antibacterial drugs is an alarming problem for the scientific community. The battle against streptococci by using antimicrobial chemotherapies will depend on the design of new chemicals with high inhibitory activity, having also as low toxicity as possible. Multi-target approaches based on quantitative-structure activity relationships (mt-QSAR) have played a very important role, providing a better knowledge about the molecular patterns related with the appearance of different pharmacological profiles including antimicrobial activity. Until now, almost all mt-QSAR models have considered the study of biological activity or toxicity separately. In the present study, we develop by the first time, a unified multitasking (mtk) QSAR model for the simultaneous prediction of anti-streptococci activity and toxic effects against biological models like Mus musculus and Rattus norvegicus. The mtk-QSAR model was created by using artificial neural networks (ANN) analysis for the classification of compounds as positive (high biological activity and/or low toxicity) or negative (otherwise) under diverse sets of experimental conditions. Our mtk-QSAR model, correctly classified more than 97% of the cases in the whole database (more than 11,500 cases), serving as a promising tool for the virtual screening of potent and safe anti-streptococci drugs.
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28
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Derivatives in discrete mathematics: a novel graph-theoretical invariant for generating new 2/3D molecular descriptors. I. Theory and QSPR application. J Comput Aided Mol Des 2012; 26:1229-46. [DOI: 10.1007/s10822-012-9591-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2012] [Accepted: 07/19/2012] [Indexed: 10/27/2022]
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29
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Jamróz MH, Rode JE, Ostrowski S, Lipiński PFJ, Dobrowolski JC. Chirality Measures of α-Amino Acids. J Chem Inf Model 2012; 52:1462-79. [DOI: 10.1021/ci300057h] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Michał H. Jamróz
- Industrial Chemistry Research
Institute, 8 Rydygiera Street, 01-793 Warsaw, Poland
| | - Joanna E. Rode
- Industrial Chemistry Research
Institute, 8 Rydygiera Street, 01-793 Warsaw, Poland
| | - Sławomir Ostrowski
- Industrial Chemistry Research
Institute, 8 Rydygiera Street, 01-793 Warsaw, Poland
| | - Piotr F. J. Lipiński
- Industrial Chemistry Research
Institute, 8 Rydygiera Street, 01-793 Warsaw, Poland
| | - Jan Cz. Dobrowolski
- Industrial Chemistry Research
Institute, 8 Rydygiera Street, 01-793 Warsaw, Poland
- National Medicines Institute,
30/34 Chełmska Street, 00-725 Warsaw, Poland
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30
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Milic̆ević A, Raos N. Estimation of Stability Constants of Copper(II) Complexes with α-Amino Acids Using Connectivity Index 3χv. Common Model for the Binary and Ternary Complexes. CHINESE J CHEM 2011. [DOI: 10.1002/cjoc.201180316] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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32
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Katritzky AR, Kuanar M, Slavov S, Hall CD, Karelson M, Kahn I, Dobchev DA. Quantitative Correlation of Physical and Chemical Properties with Chemical Structure: Utility for Prediction. Chem Rev 2010; 110:5714-89. [DOI: 10.1021/cr900238d] [Citation(s) in RCA: 386] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Alan R. Katritzky
- Center for Heterocyclic Compounds, Department of Chemistry, University of Florida, Gainesville, Florida 32611
| | - Minati Kuanar
- Center for Heterocyclic Compounds, Department of Chemistry, University of Florida, Gainesville, Florida 32611
| | - Svetoslav Slavov
- Center for Heterocyclic Compounds, Department of Chemistry, University of Florida, Gainesville, Florida 32611
| | - C. Dennis Hall
- Center for Heterocyclic Compounds, Department of Chemistry, University of Florida, Gainesville, Florida 32611
| | - Mati Karelson
- Institute of Chemistry, Tallinn University of Technology, Akadeemia tee 15, Tallinn 19086, Estonia, and MolCode, Ltd., Soola 8, Tartu 51013, Estonia
| | - Iiris Kahn
- Institute of Chemistry, Tallinn University of Technology, Akadeemia tee 15, Tallinn 19086, Estonia, and MolCode, Ltd., Soola 8, Tartu 51013, Estonia
| | - Dimitar A. Dobchev
- Institute of Chemistry, Tallinn University of Technology, Akadeemia tee 15, Tallinn 19086, Estonia, and MolCode, Ltd., Soola 8, Tartu 51013, Estonia
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33
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Quantitative structure–retention relationships of polycyclic aromatic hydrocarbons gas-chromatographic retention indices. J Chromatogr A 2010; 1217:4411-21. [DOI: 10.1016/j.chroma.2010.04.038] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2009] [Revised: 04/08/2010] [Accepted: 04/16/2010] [Indexed: 11/19/2022]
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34
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Pogliani L. Model of twelve properties of a set of organic solvents with graph-theoretical and/or experimental parameters. J Comput Chem 2010; 31:295-307. [PMID: 19462460 DOI: 10.1002/jcc.21319] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Twelve properties of a highly heterogeneous class of organic solvents have been modeled with a graph-theoretical molecular connectivity modified (MC) method, which allows to encode the core electrons and the hydrogen atoms. The graph-theoretical method uses the concepts of simple, general, and complete graphs, where these last types of graphs are used to encode the core electrons. The hydrogen atoms have been encoded by the aid of a graph-theoretical perturbation parameter, which contributes to the definition of the valence delta, delta(v), a key parameter in molecular connectivity studies. The model of the twelve properties done with a stepwise search algorithm is always satisfactory, and it allows to check the influence of the hydrogen content of the solvent molecules on the choice of the type of descriptor. A similar argument holds for the influence of the halogen atoms on the type of core electron representation. In some cases the molar mass, and in a minor way, special "ad hoc" parameters have been used to improve the model. A very good model of the surface tension could be obtained by the aid of five experimental parameters. A mixed model method based on experimental parameters plus molecular connectivity indices achieved, instead, to consistently improve the model quality of five properties. To underline is the importance of the boiling point temperatures as descriptors in these last two model methodologies.
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Affiliation(s)
- Lionello Pogliani
- Dipartimento di Chimica, Università della Calabria, via P. Bucci, 14 C, 87036 Rende, Italy.
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35
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Design of novel antituberculosis compounds using graph-theoretical and substructural approaches. Mol Divers 2009; 13:445-58. [PMID: 19340599 DOI: 10.1007/s11030-009-9129-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2008] [Accepted: 02/16/2009] [Indexed: 10/20/2022]
Abstract
The increasing resistance of Mycobacterium tuberculosis to the existing drugs has alarmed the worldwide scientific community. In an attempt to overcome this problem, two models for the design and prediction of new antituberculosis agents were obtained. The first used a mixed approach, containing descriptors based on fragments and the topological substructural molecular design approach (TOPS-MODE) descriptors. The other model used a combination of two-dimensional (2D) and three-dimensional (3D) descriptors. A data set of 167 compounds with great structural variability, 72 of them antituberculosis agents and 95 compounds belonging to other pharmaceutical categories, was analyzed. The first model showed sensitivity, specificity, and accuracy values above 80% and the second one showed values higher than 75% for these statistical indices. Subsequently, 12 structures of imidazoles not included in this study were designed, taking into account the two models. In both cases accuracy was 100%, showing that the methodology in silico developed by us is promising for the rational design of antituberculosis drugs.
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Guha R. On the interpretation and interpretability of quantitative structure–activity relationship models. J Comput Aided Mol Des 2008; 22:857-71. [DOI: 10.1007/s10822-008-9240-5] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2008] [Accepted: 08/14/2008] [Indexed: 01/28/2023]
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Warburton PL, Wang JL, Mezey PG. On the Balance of Simplification and Reality in Molecular Modeling of the Electron Density. J Chem Theory Comput 2008; 4:1627-36. [DOI: 10.1021/ct800268c] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Peter L. Warburton
- Scientific Modeling and Simulation Laboratory (SMSL), Department of Chemistry and Department of Physics and Physical Oceanography, Memorial University of Newfoundland, St. John’s, Newfoundland A1B 3X7, Canada, Molecular Graphics and Modeling Laboratory, University of Kansas, Lawrence, Kansas 66045, and Institute for Advanced Study, Collegium Budapest, Szentháromság utca 2, 1014 Budapest, Hungary
| | - Jenna L. Wang
- Scientific Modeling and Simulation Laboratory (SMSL), Department of Chemistry and Department of Physics and Physical Oceanography, Memorial University of Newfoundland, St. John’s, Newfoundland A1B 3X7, Canada, Molecular Graphics and Modeling Laboratory, University of Kansas, Lawrence, Kansas 66045, and Institute for Advanced Study, Collegium Budapest, Szentháromság utca 2, 1014 Budapest, Hungary
| | - Paul G. Mezey
- Scientific Modeling and Simulation Laboratory (SMSL), Department of Chemistry and Department of Physics and Physical Oceanography, Memorial University of Newfoundland, St. John’s, Newfoundland A1B 3X7, Canada, Molecular Graphics and Modeling Laboratory, University of Kansas, Lawrence, Kansas 66045, and Institute for Advanced Study, Collegium Budapest, Szentháromság utca 2, 1014 Budapest, Hungary
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Miličević A, Raos N. Influence of Chelate Ring Interactions on Copper(II) Chelate Stability Studied by Connectivity Index Functions. J Phys Chem A 2008; 112:7745-9. [DOI: 10.1021/jp802018m] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ante Miličević
- Institute for Medical Research and Occupational Health, Ksaverska c. 2, P.O. Box 291, HR-10000 Zagreb, Croatia
| | - Nenad Raos
- Institute for Medical Research and Occupational Health, Ksaverska c. 2, P.O. Box 291, HR-10000 Zagreb, Croatia
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García-Domenech R, Galvez J, de Julian-Ortiz JV, Pogliani L. Some new trends in chemical graph theory. Chem Rev 2008; 108:1127-69. [PMID: 18302420 DOI: 10.1021/cr0780006] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ramón García-Domenech
- Unidad de Investigación de Diseño de Farmacos y Conectividad Molecular, Departamento de Química Fisica, Facultad de Farmacía, Universitat de València, 46100 Burjassot, València, Spain
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40
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Yu Y, Dubey M, Bernasek SL, Dismukes GC. Self-assembled monolayer of organic iodine on a Au surface for attachment of redox-active metal clusters. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2007; 23:8257-63. [PMID: 17583917 DOI: 10.1021/la062785d] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
The attachment of a bifunctional iodo-organo-phosphinate compound to gold (Au) surfaces via chemisorption of the iodine atom is described and used to chelate a redox-active metal cluster via the phosphinate group. XPS, AFM, and electrochemical measurements show that (4-iodo-phenyl)phenyl phosphinic acid (IPPA) forms a tightly bound self-assembled monolayer (SAM) on Au surfaces. The surface coverage of an IPPA monolayer on Au was quantified by an electrochemical method and found to be 0.40 +/- 0.03 nmol/cm2, roughly corresponding to 0.4 monolayers. We show that the Au/IPPA SAM, but not the underivatized Au, adsorbs Mn4O4(Ph2PO2)6 from solution by a phosphinate exchange reaction to yield Au/IPPA/Mn4O4(Ph2PO2)5 SAM. The resulting SAM is firmly bound and not removed by sonication, as confirmed by manganese XPS (Mn 2p1/2) and by AFM. Electrochemistry confirms that Mn4O4(Ph2PO2)6 is anchored on the Au/IPPA surface and that redox chemistry can be mediated between the electrode and the surface-attached complex. Mn4O4(Ph2PO2)6 contains the reactive Mn4O46+ cubane core, a redox-active bioinspired catalyst.
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Affiliation(s)
- Ying Yu
- Department of Chemistry and PRISM, Princeton University, Princeton, NJ 08540, USA
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41
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Ren Y, Liu H, Yao X, Liu M. Three-dimensional topographic index applied to the prediction of acyclic C5–C8 alkenes Kováts retention indices on polydimethylsiloxane and squalane columns. J Chromatogr A 2007; 1155:105-11. [PMID: 17466321 DOI: 10.1016/j.chroma.2007.04.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2006] [Revised: 04/02/2007] [Accepted: 04/04/2007] [Indexed: 10/23/2022]
Abstract
A novel approach is described for the prediction of gas chromatographic Kováts retention indices of 150 acyclic C5-C8 alkenes on two stationary phases (polydimethylsiloxane, PDMS, and squalane, SQ). The heuristic method was used to build multiple linear regression models using descriptors calculated by MODLESLAB software and CODESSA program. The resulting quantitative structure-retention relationship (QSRR) models were well-correlated, with predictive R2 values of 0.970 and 0.958 for retention indices on PDMS and SQ columns, respectively. 1Omegap, a three-dimensional (3D) topographic index, was found to play the most important role in the description of the chromatographic retention behavior of the alkenes in these two stationary phases. Moreover, this index could completely distinguish different isomers of alkene. Therefore, it can also be extended to distinguish different isomers of other compounds so that can well describe their quantitative structure-retention relationships.
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Affiliation(s)
- Yueying Ren
- Department of Chemistry, Lanzhou University, Lanzhou 730000, China
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Acevedo-Martínez J, Escalona-Arranz JC, Villar-Rojas A, Téllez-Palmero F, Pérez-Rosés R, González L, Carrasco-Velar R. Quantitative study of the structure-retention index relationship in the imine family. J Chromatogr A 2005; 1102:238-44. [PMID: 16288769 DOI: 10.1016/j.chroma.2005.10.019] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2004] [Revised: 10/04/2005] [Accepted: 10/11/2005] [Indexed: 11/28/2022]
Abstract
The Kováts retention index is one of the most popular descriptors of the performance of organic compounds in gas chromatography (GC). The mathematical modeling of this index is an interesting and open problem in analytical chemistry. In this paper, two models for the prediction of the Kováts retention index are presented. Topologic, topographic and quantum-chemical descriptors were used as structural descriptors. Multiple linear regression (MLR) analysis provides the first model using the forward stepwise procedure for the variable selection. For the second one, an ensemble of artificial neural network (ANN) was constructed using the pruning algorithm. Both methods were validated by an external set of compounds, by the Golbraikh and Tropsha method and by the leave-one-out (LOO) and the leave many out (LMO) procedures. The R2, RMScv and Q2, values for the training sets were 0.884, 0.589 and 0.830 for NN and 0.974, 0.417 and 0.970 for MLR models, respectively. The robustness of both models was demonstrated. Both portrait the chromatographic performance of the sample but in this case, the results of MLR equation are better than the NN ones. The MLR model is recommended because of its simplicity.
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Affiliation(s)
- Jorge Acevedo-Martínez
- Dpto. Química, Fac. Ciencias Naturales, Universidad de Oriente, Patricio Lumumba s/n, Santiago de Cuba, Cuba
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Estrada E. Three-Dimensional Generalized Graph Matrix, Harary Descriptors, and a Generalized Interatomic Lennard-Jones Potential. J Phys Chem A 2004. [DOI: 10.1021/jp049139c] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ernesto Estrada
- Molecular Informatics, X-rays Unit, RIAIDT, Edificio CACTUS, University of Santiago de Compostela, Santiago de Compostela 15782, Spain
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Affiliation(s)
- Milan Randić
- National Institute of Chemistry, Ljubljana, Slovenia
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46
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Estrada E. Generalized Graph Matrix, Graph Geometry, Quantum Chemistry, and Optimal Description of Physicochemical Properties. J Phys Chem A 2003. [DOI: 10.1021/jp0346561] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ernesto Estrada
- Safety & Environmental Assurance Centre (SEAC), Unilever, Colworth House, Sharnbrook, Bedford MK44 1LQ, U.K
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47
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Netzeva TI, Schultz TW, Aptula AO, Cronin MTD. Partial least squares modelling of the acute toxicity of aliphatic compounds to Tetrahymena pyriformis. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2003; 14:265-283. [PMID: 14506870 DOI: 10.1080/1062936032000101501] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The aim of this study was to evaluate a multivariate statistical model, utilising Partial Least Squares (PLS) analysis, for the prediction of the acute toxicity of aliphatic chemicals to the ciliate Tetrahymena pyriformis. A model was developed that was capable of making a prediction regardless the mechanism of toxic action. The toxicity of 476 compounds, possessing different mechanisms of toxic action was considered. A set of 74 descriptors, including the octanol-water partition coefficient, molecular-orbital descriptors, geometrical, topological and connectivity indices, was generated. A three-component, eight-descriptor PLS model was developed. It was validated by a Y-permutation test and by simulation of external prediction for complementary subsets. A comparison with existing class or mechanism-based models, derived on the same data set, was made.
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Affiliation(s)
- T I Netzeva
- School of Pharmacy and Chemistry, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, UK
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48
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Pogliani L. Complete graph conjecture for inner-core electrons: homogeneous index case. J Comput Chem 2003; 24:1097-109. [PMID: 12759909 DOI: 10.1002/jcc.10277] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The complete graph conjecture that encodes the inner-core electrons of atoms with principal quantum number n >or= 2 with complete graphs, and especially with odd complete graphs, is discussed. This conjecture is used to derive new values for the molecular connectivity and pseudoconnectivity basis indices of hydrogen-suppressed chemical pseudographs. For atoms with n = 2 the new values derived with this conjecture are coincident with the old ones. The modeling ability of the new homogeneous basis indices, and of the higher-order terms, is tested and compared with previous modeling studies, which are centered on basis indices that are either based on quantum concepts or partially based on this new conjecture for the inner-core electrons. Two similar algorithms have been proposed with this conjecture, and they parallel the two "quantum" algorithms put forward by molecular connectivity for atoms with n > 2. Nine properties of five classes of compounds have been tested: the molecular polarizabilities of a class of organic compounds, the dipole moment, molar refraction, boiling points, ionization energies, and parachor of a series of halomethanes, the lattice enthalpy of metal halides, the rates of hydrogen abstraction of chlorofluorocarbons, and the pED(50) of phenylalkylamines. The two tested algorithms based on the odd complete graph conjecture give rise to a highly interesting model of the nine properties, and three of them can even be modeled by the same set of basis indices. Interesting is the role of some basis indices all along the model.
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Affiliation(s)
- Lionello Pogliani
- Dipartimento di Chimica, Università della Calabria, 87030 Rende (CS), Italy.
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Galvez J. Prediction of molecular volume and surface of alkanes by molecular topology. JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES 2003; 43:1231-9. [PMID: 12870916 DOI: 10.1021/ci034036x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Molecular volume and molecular surface are expressed as a function of topological degree in alkane graphs. This allows not only a straightforward approach to calculate such physicochemical magnitudes but also an interpretation of the role of the local vertex invariant (LOVI) or valence degree, delta, as well as the connectivity indices in the prediction of physicochemical properties. The interpretation is based on the concept of molecular accessibility (as introduced by Estrada, J. Phys. Chem. A 2002, 106, 9085) for which precise mathematical definitions are provided.
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Affiliation(s)
- Jorge Galvez
- Molecular Connectivity & Drug Design Research Unit, Department of Physical Chemistry, Faculty of Pharmacy, University of Valencia, Av. V.A. Estelles s.n., 46100-Burjasot, Valencia, Spain.
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50
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Estrada E, González H. What are the limits of applicability for graph theoretic descriptors in QSPR/QSAR? Modeling dipole moments of aromatic compounds with TOPS-MODE descriptors. JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES 2003; 43:75-84. [PMID: 12546541 DOI: 10.1021/ci025604w] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The numerous possibilities of using graph theoretic descriptors in QSPR/QSAR are analyzed, and some misunderstandings on the role of this theoretical approach in chemistry are clarified. Principal component analysis is used to obtain a property space for several physicochemical properties of aromatic compounds. It is proved that most of the QSPR applications of the graph-theoretic structure descriptors are concentrated to the description of properties in a very limited region of this property space. Here, we show that graph-theoretic approaches are also applicable to the modeling of physicochemical properties that are far away from this region traditionally studied. The molecular dipole moments of benzene derivatives, mono-, ortho-, meta-, and para-susbtituted, are modeled by using the Topological Sub-Structural Molecular Design (TOPS-MODE) approach. The TOPS-MODE approach used permits to calculate group dipole moments that are given for several substituents. The differences between these group dipoles and those obtained by simple difference between experimental values are analyzed. Some difficulties arising from this traditional way of deriving substituent constants are identified and analyzed.
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Affiliation(s)
- Ernesto Estrada
- Faculty of Pharmacy, Department of Organic Chemistry, University of Santiago de Compostela, Santiago de Compostela 15706, Spain.
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